SOISOS

How to plot density
plot(density(DATA))

Rainbow color in R
If you want to make a plot have rainbow color range, you can use rainbow function:

rcol=rainbow(length(YOURDATA))
plot(DATAX, DATAY, type=”l”)
points(DATAX, DATAY, pch=16, col=rcol)

Simple Plot

How to change the size of text in a plot?
Use argument cex.[attribute] , and examples are below:

main titles by cex.main
sub titles by cex.sub
axis annonation by cex.axis
xlab and ylab by cex.lab

Legend
legend(x, y = NULL, legend, fill = NULL, col = par(“col”),
border=”black”, lty, lwd, pch,
angle = 45, density = NULL, bty = “o”, bg = par(“bg”),
box.lwd = par(“lwd”), box.lty = par(“lty”), box.col = par(“fg”),
pt.bg = NA, cex = 1, pt.cex = cex, pt.lwd = lwd,
xjust = 0, yjust = 1, x.intersp = 1, y.intersp = 1,
adj = c(0, 0.5), text.width = NULL, text.col = par(“col”),
merge = do.lines && has.pch, trace = FALSE,
plot = TRUE, ncol = 1, horiz = FALSE, title = NULL,
inset = 0, xpd, title.col = text.col, title.adj = 0.5)

To eliminate rows with condition

# eliminate rows that Age is empty
dat<-dat[-which(temp$Age==""),]

How to create contingency table from categorical data in r.

Example:
There are three categorical variables x1, x2, x3 measured from wild cats where
x1 = gender (male, female)
x2 = age (young, kitten, adult)
x3 = test result ( positive = 1, negative =0).

r table will generate two tables: 2by2 table for each of x3=0 and x3=1.

# r code
table(x1, x2, x3)

As shown below, the R output has two parts when x3=0 and x3=1.
Row represents Gender (x1) and the column represents Age (x2).
The numbers are counts of cats that fall into the corresponding categories.

, , = 0


A K Y
F 14 84 2
M 8 97 2

, , = 1


A K Y
F 1 12 0
M 1 36 0

Nonparametric classification method
Idea behind knn is that you measure distance between new value (x0) and each of the neighboring points and count the first k shortest distances, then classify the new value to the group that wins the majority rule.

Steps:
1. Choose k as an odd integer
2. Measure the distance between xo and each of the training data points
3. Order the distance
4. Select first k distances
5. Assign the new value to the group that wins the majority rule

R Code for KNN

# importing data into a dataframe
iris.dat <- read.table("iris_short.txt", header=T)

# legend (#xcoord, #ycoord, col=c("colors"), pch=c("shape of points"), text.col=c("textcolor")
# legend=c("actual text you want to use")
legend(4.5, 4.9, col=c("red", "darkgreen"), pch=c(1,1), text.col=c("red", "darkgreen"), legend=c("Setosa", "Versicolor"))

# library class is required for knn
library(class)

# generating 100 data points in the range of (4.3, 7.0) and (1.0, 5.1)
x1<-seq(4.3, 7.0, len=100)
x2<-seq(1.0, 5.1, len=100)
x1.new<-rep(x1, 100)
x2.new<-rep(x2, rep(100,100))
iris.knn.2<-knn(iris.dat[,2:3], cl=iris.dat$species, test=cbind(x1.new, x2.new), k=2)

## plotting k nearest neighbors
# pt.col is color that will be assigned to each point based on what knn classifies the data as
# iris.knn.2 will have either 1 or 2.
# if iris.knn.2 >1, then take darkgreen, red o.w
pt.col<- ifelse(c(iris.knn.2) > 1, "darkgreen", "red")

# drawing contour
contour(x1,x2,matrix(iris.knn.2,nc=100),add=T,nlevel=1,lty=1,drawlabel=F)


Preparation and EDA
Data should be standardized in factor analysis
scale(crime.dat)

#standardize data
crime.dat.sd= scale(crime.dat)

To obtain number of factors to use for the factor analysis, PCA can be used
#PCA for EDA
crime.pca<-princomp(crime.dat.sd)

Bartlett scores
crime.fa.s<- factanal(crime.dat.sd, 3, scores="Bartlett", rotation="varimax")
crime.fa.s$scores

Factor Analysis

#arg(standarized data, no of factors, rotation)
factanal(crime.da.sd, 3, rotation="none"

Hypothesis Testing
H₀: The number of factor is sufficient
H_a: The number of Factor is not sufficient

Decision Rule
Reject H₀ if test statistic > Chiq(alpha, df) or if p-value is small
[Note: the test statistic and p-value can be obtained from R output of factoranal]

Performing a PCA after standardizing the variables and obtain estimates for the principal components for the standardized variables.

Reading in athelete’s data
ath.dat <- read.table("athelete.txt")

Standardizing the data
ath.dat.std <- scale(ath.dat)

Correlation matrix (since covariance of standardized data is correlation)
R = cov(ath.dat.std)

Eigen Values
lambda = eigen(R)$val

Eigen values are read to assess which components explain the variance the most. In this case, the first two show values above 1 therefore we will take the first two components.

[1] 1.0900625 1.0290211 0.8809163

Eigen Vector
es= eigen(R)$vec

[,1] [,2] [,3]
[1,] 0.7476122 -0.1215134 -0.6529246
[2,] -0.2827011 0.8313790 -0.4784235
[3,] 0.6009626 0.5422577 0.5871971

Three eigen vectors associated with the labmda values. The three vectors are eigen vectors of the covariance matrix and also the loadings of Principle components.

You can find the loadings (eigen vectors) by obtaining loadings of the princomp output

loadings(ath.pca)

Loadings:
Comp.1 Comp.2 Comp.3
X1 0.748 -0.122 -0.653
X2 -0.283 0.831 -0.478
X3 0.601 0.542 0.587